Import and export data

.io contains functions to import user data ready for use with Pytzer, and export the results of your calculations.

.getmols - import CSV dataset

Imports a table of temperature, pressure and molality data, formatted ready for Pytzer's model functions. For calculations without equilibration, where the concentration of every individual solute is specified in the input file.

Syntax:

>>> mols, ions, tempK, pres = pz.io.getmols(filename, delimiter=',', skip_top=0)

Inputs:

  • filename - path and name of a text file containing a set of solution compositions and corresponding temperatures. See full decription below;
  • delimiter - column delimiter. Optional; defaults to ','.
  • skip_top - number of rows in filename above the row containing the headers described below. Optional; defaults to 0.

The file should be in comma-separated variable (CSV) format, but if another separator is used this can be specified with delimiter. The contents should be formatted as follows:

  • the first row provides the header for each column;
  • each column represents the concentration of a different ion (or the temperature or pressure);
  • each row characterises a different solution composition.

The header of the column containing the temperatures (always in K) must be tempK, and the pressures (always in dbar) must be headed with pres. The order of the columns does not matter. The other columns should be headed with the chemical symbol for the ion, excluding the charge, and without any brackets. Only internal stoichiometry should be included: $\ce{SO4^2-}$ becomes SO4; $\ce{Na+}$ becomes Na, and would not be Na2 even if a solution of $\ce{Na2SO4}$ was under investigation. For a more detailed explanation, see the naming conventions.

For example, to specify these solutions:

  • $\ce{NaCl}$ at 0.10, 3.00 and 6.25 mol·kg−1;
  • $\ce{KCl}$ at 0.50 and 3.45 mol·kg−1;
  • a mixture containing 1.20 mol·kg−1 $\ce{NaCl}$ and 0.80 mol·kg−1 $\ce{KCl}$;
  • $\ce{Na2SO4}$ at 2.00 mol·kg−1;
  • all at 298.15 K, and 1 atm (i.e. 10.1325 dbar);

we could use this CSV file:

tempK , pres   , Na  , K   , Cl  , SO4
298.15, 10.1325, 0.10,     , 0.10,
298.15, 10.1325, 3.00,     , 3.00,
298.15, 10.1325, 6.25,     , 6.25,
298.15, 10.1325,     , 0.50, 0.50,
298.15, 10.1325,     , 3.45, 3.45,
298.15, 10.1325, 1.20, 0.80, 2.00,
298.15, 10.1325, 4.00,     ,     , 2.00

Note: oceanographers typically record pressure within the ocean as only due to the water, so at the sea surface the pressure would be 0 dbar. However, the atmospheric pressure (1 atm = 10.1325 dbar) should also be taken into account for calculations within Pytzer.

Outputs:

  • mols - concentrations (molality) of solutes in mol·kg−1. Each row represents a different ion, while each column characterises a different solution composition;
  • ions - list of the solute codes, corresponding to the rows in mols;
  • tempK - solution temperature in K. Each value corresponds to the matching column in mols;
  • pres - solution pressure in dbar. Each value corresponds to the matching column in mols.

.gettots - import CSV dataset

Imports a table of temperature, pressure and molality data, formatted ready for Pytzer's equilibration functions. For calculations with equilibration, where some solution components are given as totals.

Syntax:

>>> tots, mols, eles, ions, tempK, pres = pz.io.gettots(filename, delimiter=',', skip_top=0)

Inputs:

  • filename - path and name of a text file containing a set of solution compositions and corresponding temperatures. See full decription below;
  • delimiter - column delimiter. Optional; defaults to ','.
  • skip_top - number of rows in filename above the row containing the headers described below. Optional; defaults to 0.

The file should be in comma-separated variable (CSV) format, and its contents follow the same rules as for the getmols function above. However, it may also include total concentrations for solutes that are in dynamic equilibria to be solved. These are indicated by prefixing the solute name with t_ in the header row.

Outputs:

  • tots - total concentrations (molality) of equilibrating solutes in mol·kg−1. Each row represents a different set of solutes, while each column characterises a different solution composition;
  • mols - concentrations (molality) of non-equilibrating solutes in mol·kg−1. Each row represents a different solute, while each column characterises a different solution composition;
  • eles - list of the solute codes corresponding to the rows in tots;
  • ions - list of the solute codes corresponding to the rows in mols;
  • tempK - solution temperature in K. Each value corresponds to the matching column in mols;
  • pres - solution pressure in dbar. Each value corresponds to the matching column in mols.

.saveall - save to CSV

Saves the results of all calculations to a CSV file, with a format similar to that described for the input file above.

Syntax:

>>> pz.io.saveall(filename, mols, ions, tempK, pres, osm, aw, acfs)

Inputs:

The input filename gives the name of the file to save, including the path. The file will be overwritten if it already exists, or created if not. It should end with .csv.

The other variables are the inputs mols, ions, tempK and pres exactly as created by the data import function above, while osm, aw and acfs are the results of the corresponding model functions.